Align 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase
Query= metacyc::MONOMER-20632 (478 letters) >FitnessBrowser__Dyella79:N515DRAFT_3729 Length = 483 Score = 297 bits (761), Expect = 5e-85 Identities = 189/451 (41%), Positives = 243/451 (53%), Gaps = 9/451 (1%) Query: 28 TNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEVRSDLLDKVGSTIIARSADIGRLL 87 T +V A P A+VDAAV AA A P WA E R+ LL ++ I AR + L Sbjct: 30 TGEVFAHCPESSFADVDAAVAAAVAAAPGWAATPSEQRARLLQRLADLIEARLDEFAALE 89 Query: 88 AREEGKTLAEGIGETV-RAGRIFKYFAGEALRRHGQNLESTRPGVEIQTYRQAVGVYGLI 146 +R+ GK L+ + RA +YFA A+ + G T RQ +GV I Sbjct: 90 SRDSGKPLSLARSLDIPRAVSNLRYFAA-AIVPWSSESHAMELGAINYTLRQPLGVVACI 148 Query: 147 TPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATANVLADIMAECGAPAGVFNMLFGRG 206 +PWN P+ + WK APALA GN VV KP+ TP TA +L ++ E G P GV N++ GRG Sbjct: 149 SPWNLPLYLFTWKIAPALAAGNAVVAKPSEITPCTAALLGELSIEAGFPPGVLNIVQGRG 208 Query: 207 -SMGDALIKHKDVDGVSFTGSQGVGAQVAAAAVARQARVQLEMGGKNPLIVLDDADLERA 265 +G AL++H+DV VSFTGS GAQ+AAAA R ++ LE+GGKNP IV DADL A Sbjct: 209 PEVGQALVEHRDVKAVSFTGSTRTGAQIAAAAAPRFKKLSLELGGKNPAIVFADADLSDA 268 Query: 266 VAIALDGSFFAT-GQRCTASSRLIVQDGIHDKFVALLAEKVAALRVGDALDPNTQIGPAV 324 + S FA G+ C SRL+VQ I+D F KV ALRVGD + T +G V Sbjct: 269 NLDTIVRSGFANQGEICLCGSRLLVQRSIYDAFRERYLAKVRALRVGDPREAATDLGALV 328 Query: 325 SEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNP---GWYVRPTLIADTQAGMRINNEEV 381 S + + I A +EGGRV+ GGD + L P GWYV PT+I N +E+ Sbjct: 329 SREHFDKVTGCIAQARAEGGRVLCGGDALALPGPLAGGWYVAPTVIEGLGPETATNQQEI 388 Query: 382 FGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSLKHARHFQRYARAGMTMVNLATAGV 441 FGPV + I +AL IANG +GL+A + TT L A F G+ +N Sbjct: 389 FGPVVTLIPFDDEAQALAIANGTGYGLAASLWTTDLSRAHRFGAQLDFGIVWINCWLLR- 447 Query: 442 DYHVPFGGTKSSSYGAREQGFAAVEFFTQTK 472 D PFGG K S G RE G A+ FFT+ K Sbjct: 448 DLRTPFGGAKQSGVG-REGGVEALRFFTEPK 477 Lambda K H 0.317 0.133 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 551 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 478 Length of database: 483 Length adjustment: 34 Effective length of query: 444 Effective length of database: 449 Effective search space: 199356 Effective search space used: 199356 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory